Curator Dashboard

Knowledge engineering software for reasoning with scientific observations and interpretations. The software has three parts: (a) the KEfED model editor - a design editor for creating KEfED models by drawing a flow diagram of an experimental protocol; (b) the KEfED data interface - a spreadsheet-like tool that permits users to enter experimental data pertaining to a specific model; (c) a "neural connection matrix" interface that presents neural connectivity as a table of ordinal connection strengths representing the interpretations of tract-tracing data. This tool also allows the user to view experimental evidence pertaining to a specific connection. The KEfED model is designed to provide a lightweight representation for scientific knowledge that is (a) generalizable, (b) a suitable target for text-mining approaches, (c) relatively semantically simple, and (d) is based on the way that scientist plan experiments and should therefore be intuitively understandable to non-computational bench scientists. The basic idea of the KEfED model is that scientific observations tend to have a common design: there is a significant difference between measurements of some dependent variable under conditions specified by two (or more) values of some independent variable.

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• SciCrunch
• 16 years ago - by Anonymous

Set of software modules for performing common ChIP-seq data analysis tasks across the whole genome, including positional correlation analysis, peak detection, and genome partitioning into signal-rich and signal-poor regions. The tools are designed to be simple, fast and highly modular. Each program carries out a well-defined data processing procedure that can potentially fit into a pipeline framework. ChIP-Seq is also freely available on a Web interface.

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• SciCrunch
• 13 years ago - by Anonymous

A suite of software tools for analyzing and manipulating next-generation sequencing datasets, such as FASTQ, BED and BAM format files. These tools provide a stable and modular platform for data management and analysis.

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• SciCrunch
• 13 years ago - by Anonymous

Software package for working with VCF files. Used to provide easily accessible methods for working with complex genetic variation data in the form of VCF files.Implements various utilities for processing Variant Call Format files, including validation, merging, comparing. Provides general Perl API.

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• SciCrunch
• 13 years ago - by Anonymous

Service that provides a comprehensive compilation of variant knowledge that allows you to identify pathogenic variants in human whole genome or exome sequences. It makes it easy to upload a complete genome?s worth of variations and identify the biologically relevant subset of known mutations, mutations that are novel and appear in a candidate disease genes, or mutations that are predicted to have a deleterious effect. The database includes a comprehensive collection of disease causing mutations from HGMD Professional, regulatory sites from TRANSFAC , and disease genes, drug targets and pathways from PROTEOME, as well as pharmacogenomic variants. It integrates the best public data-sets on somatic mutations, allele frequencies and clinical variants, in their most up-to-date version, for a total of more than 165 million annotations. It is possible to identify known pathogenic variants, remove harmless common variants, and obtain deleterious predictions for novel variants. With family data, it is possible to identify variants that are de novo, compound heterozygous only in the offspring. All of the results can be downloaded to Excel for further review. For core facilities and bioinformaticians, the complete underlying data is made available for download and easy integration into custom analysis pipelines. Genome Trax data is optimized to work with many other software packages, such as ANNOVARTM, CLC bio, Alamut, SimulConsult, and Cartagenia.

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• SciCrunch
• 13 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025.Software to classify the function and phylogeny of reads as short as 30 bp. It is flexible, which can utilize multiple data modules and downstream analysis scripts. It is fast, reading in signature lists of 5-500 million peptide signatures in 1-15 minutes, and subsequently processes genomic fragments at the rate of 6 Gbp/hr. It parallelizes without significant increase in memory requirements until I/O bound on multiple input files; parallelization works well on 64 processors.

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• SciCrunch
• 13 years ago - by Anonymous

Software that gives estimates of the structure and diversity of uncultured viral communities using metagenomic information.

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• SciCrunch
• 12 years ago - by Anonymous

A C++ library for parsing and manipulating Variant Call Format (VCF) files, and many command-line utilities. The API provides a quick and extremely permissive method to read and write VCF files. Extensions and applications of the library provided in the included utilities (*.cpp) comprise the vast bulk of the library's utility for most users.

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• SciCrunch
• 13 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025. Sequence analysis software for molecular biologists.

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• SciCrunch
• 13 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May,10, 2021.Software providing a visually oriented tile based approach to error detection for Solexa next-gen sequencing data. It is written in R and has both qualitative and quantitative error detection features. This software was written with the idea that the researcher's visual pattern recognition is the best way to detect novel errors and contains variety of ways to visualize that data. Once a new type of error is identified the data extraction features of the program may then be used as a starting point for the programmatic detection and/or filtration of similar errors. A supplementary role of tileQC is to convert the Eland and Q-score data contained within the Solexa "*_prb.txt" and "*_eland_results.txt" text files to a more flexible database form. Once in database form, tileQC simplifies the mechanics of interacting with that data and supplements standard SQL with an expression subsitution mechanism that allows R to be easily comingled with SQL. This system requires access to a mySQL server and the R package RMySQL as well as a few standard UNIX tools (also available on Windows and Macintosh).

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• SciCrunch
• 13 years ago - by Anonymous

Quality assessment software tool for evaluating and comparing genome assemblies. It works both with and without a given reference genome. It produces many reports, summary tables and plots.

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• SciCrunch
• 13 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025. A web-based plant genome assembly simulation platform whose resources include out of the box scripts for analyzing assembly data, an on-demand web graphing tool to model your experiment, and a downloadable database with metrics and parameters from over 3,000 simulated genome assemblies.

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• SciCrunch
• 13 years ago - by Anonymous

Blog devoted to reporting, analyzing and interpreting the latest results in the field of brain imaging technologies, particularly at the levels of systems, circuits, single cells and below. The site content is produced by Andrew Hires.

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• SciCrunch
• 16 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025. Software tools for meta-analysis in the presence of hierarchical (and/or sampling) dependence, including with gene expression studies.

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• SciCrunch
• 13 years ago - by Anonymous

A contract research organization providing drug development and animal testing services. Under the name Covance Research Products Inc., based in Denver, Pennsylvania, the company also deals in the import, breeding and sale of laboratory animals. It breeds dogs, rabbits, guinea pigs, non-human primates, and pigs, and runs the largest non-human primate laboratory in Germany. (Wikipedia)

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• SciCrunch
• 12 years ago - by Anonymous

A software package for meta-analysis of high-throughput experiments using feature annotations. It calculates significant annotations (categories) in each of two (or more) feature (i.e. gene) lists, determines the overlap between the annotations, and returns graphical and tabular data about the significant annotations and which combinations of feature lists the annotations were found to be significant. Interactive exploration is facilitated through the use of RCytoscape (heavily suggested).

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• SciCrunch
• 13 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025. Software for secondary and tertiary analysis of Next Generation Sequencing (NGS) data.

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• SciCrunch
• 13 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025. R extension whose functions are intended for cross-study comparison of gene expression array data. Required from the user is gene expression matrices, their corresponding gene-id vectors and other useful information, and they could be "list", "matrix", or "ExpressionSet". The main function is "mergeExprs" which transforms the input objects into data in the merged format, such that common genes in different datasets can be easily found. And the function "intcor" calculate the correlation coefficients. Other functions use the output from "modelOutcome" to graphically display the results and cross-validate associations of gene expression data with survival.

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• SciCrunch
• 13 years ago - by Anonymous

An ion channel focused Contract Research Organization (CRO) that does safety testing and screening for global pharma and biotech companies. ChanTest has developed a complete library of validated human ion channel-expressing cell lines to serve all the ion channel needs of its pharmaceutical and biotech customers. Services range from early functional screens for profiling drug candidates or ranking within profiles during the drug-discovery process to a complete set of in vitro GLP service products for cardiac risk assessment. ChanTest works in partnership with customers to speed the drug-development process, save time and money, and ultimately to help make better, safer drugs.

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• SciCrunch
• 14 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented November 4, 2015. Web application based on the TM4 Microarray Software Suite to provide a means of normalization and analysis of microarray data. Users can upload data in the form of Affymetrix CEL files, and define an analysis pipeline by selecting several intuitive options. It performs data normalization (eg RMA), basic statistical analysis (eg t-test, ANOVA), and analysis of annotation using gene classification (eg Gene Ontology term assignment). The analysis are performed without user intervention and the results are presented in a web-based summary that allows data to be downloaded in a variety of formats compatible with further directed analysis.

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• SciCrunch
• 13 years ago - by Anonymous